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Yorodumi- PDB-4r3b: Crystal structure of SHV-1 b-lactamase in complex with 6b-(hydrox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r3b | ||||||
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Title | Crystal structure of SHV-1 b-lactamase in complex with 6b-(hydroxymethyl)penicillanic acid sulfone PSR-283A | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE / Class A beta-lactamase / Inactivate b-lactam antibiotics | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.366 Å | ||||||
Authors | Rodkey, E.A. / van den Akker, F. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Detecting a Quasi-stable Imine Species on the Reaction Pathway of SHV-1 beta-Lactamase and 6 beta-(Hydroxymethyl)penicillanic Acid Sulfone. Authors: Che, T. / Rodkey, E.A. / Bethel, C.R. / Shanmugam, S. / Ding, Z. / Pusztai-Carey, M. / Nottingham, M. / Chai, W. / Buynak, J.D. / Bonomo, R.A. / van den Akker, F. / Carey, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r3b.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r3b.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 4r3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/4r3b ftp://data.pdbj.org/pub/pdb/validation_reports/r3/4r3b | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28907.018 Da / Num. of mol.: 1 / Fragment: SHV-1 beta-lactamase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, shv1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AD64, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | ChemComp-3GE / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 21-30% PEG6000, 0.1M HEPES pH 6.2-8.2, 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K PH range: 6.8-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 26, 2010 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.366→50 Å / Num. all: 46988 / Num. obs: 46331 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.366→1.42 Å / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.366→27.73 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.647 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.951 Å2
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Refinement step | Cycle: LAST / Resolution: 1.366→27.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.366→1.402 Å / Total num. of bins used: 20
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